The Metropolitan Police Commissioner held a 50-minute meeting with former chief whip Mr Mitchell in his Commons office.
Mr Mitchell became involved in a heated confrontation with police officer Toby Rowland, after he was refused permission to cycle through the main gate.
Pc Keith Wallis faces a possible prison sentence tomorrow after he admitted a charge of misconduct in public office for sending a letter to MP John Randall, Mr Mitchell's deputy chief whip, claiming to have witnessed the row.
Mr Mitchell said: "I am grateful to the Metropolitan Police Commissioner for his apology. We had a constructive discussion about police reform and agreed on the importance of drawing a line under this matter and looking to the future."
The Sutton Coldfield MP, who was forced to quit as chief whip over the debacle, admitted swearing but denied using the word "pleb".
Mr Justice Sweeney warned Wallis, 53, of West Drayton, west London, that "all sentencing options remain open to the court".